Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes

Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation

Biological control of the millet head miner Heliocheilus albipunctella in the Sahelian region by augmentative releases of the parasitoid wasp Habrobracon hebetor: effectiveness and farmers’ perceptions

On-farm augmentative releases of the parasitoid Habrobracon hebetor (Say) for controlling the millet head miner (MHM) Heliocheilus albipunctella (de Joannis) were tested in Burkina Faso, Mali and Niger from 2007 to 2009. In addition, a survey of farmers’ perceptions of insect pests, with particular focus on MHM, and the biological control program (BCP) was carried out. There was a significant increase of MHM parasitization rate after the releases, with up to 97% mortality. The survey on farmers’ perceptions revealed a fair knowledge of the MHM and the ability of farmers to describe the pest and the damage it caused. Farmers claimed that the biocontrol agent H. hebetor is effective and perceived a significant gain in grain yield due to this control strategy. Implications of these findings for a large extension of the MHM biocontrol program are discussed

Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.This article is from PLOS ONE; 6 (2011); e 16444; doi:10.1371/journal.pone.0016444</p

Development of Reference Transcriptomes for the Major Field Insect Pests of Cowpea: A Toolbox for Insect Pest Management Approaches in West Africa

<div><p>Cowpea is a widely cultivated and major nutritional source of protein for many people that live in West Africa. Annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, <i>Anoplocnemis curvipes</i> Fabricius (Hemiptera: Coreidae) and <i>Clavigralla tomentosicollis</i> Stål (Hemiptera: Coreidae); as well as phloem-feeding cowpea aphids, <i>Aphis craccivora</i> Koch (Hemiptera: Aphididae) and flower thrips, <i>Megalurothrips sjostedti</i> Trybom (Thysanoptera: Thripidae). Efforts to control these pests remain a challenge and there is a need to understand the structure and movement of these pest populations in order to facilitate the development of integrated pest management strategies (IPM). Molecular tools have the potential to help facilitate a better understanding of pest populations. Towards this goal, we used 454 pyrosequencing technology to generate 319,126, 176,262, 320,722 and 227,882 raw reads from <i>A. curvipes</i>, <i>A. craccivora</i>, <i>C. tomentosicollis</i> and <i>M. sjostedti</i>, respectively. The reads were <i>de novo</i> assembled into 11,687, 7,647, 10,652 and 7,348 transcripts for <i>A. curvipes</i>, <i>A. craccivora</i>, <i>C. tomentosicollis</i> and <i>M. sjostedti</i>, respectively. Functional annotation of the resulting transcripts identified genes putatively involved in insecticide resistance, pathogen defense and immunity. Additionally, sequences that matched the primary aphid endosymbiont, <i>Buchnera aphidicola</i>, were identified among <i>A. craccivora</i> transcripts. Furthermore, 742, 97, 607 and 180 single nucleotide polymorphisms (SNPs) were respectively predicted among <i>A. curvipes</i>, <i>A. craccivora</i>, <i>C. tomentosicollis</i> and <i>M. sjostedti</i> transcripts, and will likely be valuable tools for future molecular genetic marker development. These results demonstrate that Roche 454-based transcriptome sequencing could be useful for the development of genomic resources for cowpea pest insects in West Africa. </p> </div

Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae)

The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.This article is from PLOS ONE; 6 (2011); e21388; doi: 10.1371/journal.pone.0021388</p

Gene ontology classification into biological process, cellular component and molecular function.

<p>Gene ontology terms were determined using an e-value of ≤ 1.0 e-6 sorted based on level 2 classifications in all the contigs of (a) <i>A. curvipes</i>, (b) <i>A. craccivora</i>, (c) <i>C. tomentosicollis</i>, (d) <i>M. sjostedti</i>.</p

Transcripts putatively involved in responses to xenobiotic (e.g., insecticide resistance) and disease transmission in (a) <i>A. curvipes</i>, (b) <i>A. craccivora</i>, (c) <i>C. tomentosicollis</i>, (d) <i>M. sjostedti</i>.

<p>Transcripts putatively involved in responses to xenobiotic (e.g., insecticide resistance) and disease transmission in (a) <i>A. curvipes</i>, (b) <i>A. craccivora</i>, (c) <i>C. tomentosicollis</i>, (d) <i>M. sjostedti</i>.</p